Multiple sequence alignment - TraesCS2B01G175100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G175100 chr2B 100.000 3047 0 0 1 3047 150340249 150337203 0.000000e+00 5627.0
1 TraesCS2B01G175100 chr2B 98.784 1151 14 0 735 1885 150387880 150386730 0.000000e+00 2049.0
2 TraesCS2B01G175100 chr2B 86.706 1369 156 17 838 2191 150201489 150200132 0.000000e+00 1496.0
3 TraesCS2B01G175100 chr2B 86.077 1300 143 19 907 2191 150142102 150140826 0.000000e+00 1363.0
4 TraesCS2B01G175100 chr2B 85.874 1253 144 19 907 2135 150119194 150117951 0.000000e+00 1303.0
5 TraesCS2B01G175100 chr2B 97.335 638 16 1 1882 2518 150360659 150360022 0.000000e+00 1083.0
6 TraesCS2B01G175100 chr2B 97.796 499 4 1 247 738 150388690 150388192 0.000000e+00 854.0
7 TraesCS2B01G175100 chr2B 94.022 552 19 5 2510 3047 150359502 150358951 0.000000e+00 824.0
8 TraesCS2B01G175100 chr2B 98.413 252 1 1 1 252 150394259 150394011 1.000000e-119 440.0
9 TraesCS2B01G175100 chr2B 81.499 427 34 20 1 397 150202337 150201926 2.950000e-80 309.0
10 TraesCS2B01G175100 chr2B 83.483 333 39 12 497 827 150201859 150201541 2.300000e-76 296.0
11 TraesCS2B01G175100 chr2B 80.529 416 38 20 7 398 150120520 150120124 2.310000e-71 279.0
12 TraesCS2B01G175100 chr2B 85.377 212 22 5 508 719 150144876 150144674 8.560000e-51 211.0
13 TraesCS2B01G175100 chr2D 95.708 1491 60 1 840 2326 98708869 98707379 0.000000e+00 2396.0
14 TraesCS2B01G175100 chr2D 86.608 1374 153 21 838 2191 98673776 98672414 0.000000e+00 1489.0
15 TraesCS2B01G175100 chr2D 84.598 1357 159 24 861 2191 98668434 98667102 0.000000e+00 1303.0
16 TraesCS2B01G175100 chr2D 85.703 1252 143 17 907 2135 98659736 98658498 0.000000e+00 1288.0
17 TraesCS2B01G175100 chr2D 93.200 500 16 9 1 482 98709824 98709325 0.000000e+00 719.0
18 TraesCS2B01G175100 chr2D 83.610 421 29 16 1 397 98674612 98674208 2.890000e-95 359.0
19 TraesCS2B01G175100 chr2D 89.474 247 11 7 538 782 98709313 98709080 6.390000e-77 298.0
20 TraesCS2B01G175100 chr2D 83.631 336 32 13 497 827 98674145 98673828 8.260000e-76 294.0
21 TraesCS2B01G175100 chr2D 78.008 532 67 29 198 719 98669712 98669221 3.840000e-74 289.0
22 TraesCS2B01G175100 chr2D 82.258 248 27 6 7 246 98662527 98662289 6.660000e-47 198.0
23 TraesCS2B01G175100 chr2D 82.432 148 15 8 252 398 98661585 98661448 5.340000e-23 119.0
24 TraesCS2B01G175100 chr2A 85.766 1377 155 23 839 2191 97549602 97548243 0.000000e+00 1419.0
25 TraesCS2B01G175100 chr2A 86.151 1307 149 18 907 2191 97308660 97307364 0.000000e+00 1382.0
26 TraesCS2B01G175100 chr2A 85.329 1261 141 25 839 2080 97316479 97315244 0.000000e+00 1264.0
27 TraesCS2B01G175100 chr2A 80.886 858 96 41 1 827 97550476 97549656 5.580000e-172 614.0
28 TraesCS2B01G175100 chr2A 80.698 860 93 39 1 827 97317352 97316533 4.350000e-168 601.0
29 TraesCS2B01G175100 chr2A 80.564 319 26 18 105 398 97311462 97311155 2.380000e-51 213.0
30 TraesCS2B01G175100 chr6A 84.010 419 43 10 2196 2613 31029329 31029724 6.160000e-102 381.0
31 TraesCS2B01G175100 chr3A 83.679 386 40 7 2224 2609 368368482 368368120 2.910000e-90 342.0
32 TraesCS2B01G175100 chr3A 90.826 109 9 1 2501 2609 115072418 115072525 8.800000e-31 145.0
33 TraesCS2B01G175100 chr3D 80.645 93 8 7 252 343 19840076 19840159 2.540000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G175100 chr2B 150337203 150340249 3046 True 5627.000000 5627 100.000000 1 3047 1 chr2B.!!$R1 3046
1 TraesCS2B01G175100 chr2B 150386730 150388690 1960 True 1451.500000 2049 98.290000 247 1885 2 chr2B.!!$R7 1638
2 TraesCS2B01G175100 chr2B 150358951 150360659 1708 True 953.500000 1083 95.678500 1882 3047 2 chr2B.!!$R6 1165
3 TraesCS2B01G175100 chr2B 150117951 150120520 2569 True 791.000000 1303 83.201500 7 2135 2 chr2B.!!$R3 2128
4 TraesCS2B01G175100 chr2B 150140826 150144876 4050 True 787.000000 1363 85.727000 508 2191 2 chr2B.!!$R4 1683
5 TraesCS2B01G175100 chr2B 150200132 150202337 2205 True 700.333333 1496 83.896000 1 2191 3 chr2B.!!$R5 2190
6 TraesCS2B01G175100 chr2D 98707379 98709824 2445 True 1137.666667 2396 92.794000 1 2326 3 chr2D.!!$R3 2325
7 TraesCS2B01G175100 chr2D 98667102 98674612 7510 True 746.800000 1489 83.291000 1 2191 5 chr2D.!!$R2 2190
8 TraesCS2B01G175100 chr2D 98658498 98662527 4029 True 535.000000 1288 83.464333 7 2135 3 chr2D.!!$R1 2128
9 TraesCS2B01G175100 chr2A 97548243 97550476 2233 True 1016.500000 1419 83.326000 1 2191 2 chr2A.!!$R2 2190
10 TraesCS2B01G175100 chr2A 97307364 97317352 9988 True 865.000000 1382 83.185500 1 2191 4 chr2A.!!$R1 2190

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
27 28 2.398498 CAGCTGGAGAATCGAATACCG 58.602 52.381 5.57 0.0 40.25 4.02 F
1096 5461 0.684535 TTGTCCTCGTGAGCATTGGA 59.315 50.000 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 5884 0.108186 TTGCTATGCCACTCTCACCG 60.108 55.0 0.0 0.00 0.00 4.94 R
2218 14373 0.598562 AGGATGACGAATAGCGCGAT 59.401 50.0 12.1 5.99 46.04 4.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.398498 CAGCTGGAGAATCGAATACCG 58.602 52.381 5.57 0.00 40.25 4.02
556 1463 6.457851 ACTTTACGTATGTTTTCGTTCTCC 57.542 37.500 0.00 0.00 40.70 3.71
886 5228 5.186021 AGAGAACTTGTCATCGGTTCACTAT 59.814 40.000 12.90 0.00 40.97 2.12
1096 5461 0.684535 TTGTCCTCGTGAGCATTGGA 59.315 50.000 0.00 0.00 0.00 3.53
1510 5884 2.588034 GGTGCCGGCGAAGGATAC 60.588 66.667 23.90 12.38 0.00 2.24
2361 14516 1.203994 ACCGGTCTATGTTCCGTGAAG 59.796 52.381 0.00 0.00 44.51 3.02
2469 14624 2.557317 CACCAACGTCAGGTTACAACT 58.443 47.619 9.71 0.00 37.23 3.16
2508 14663 6.663093 AGCCCATATGTTCAGATTACAACAAA 59.337 34.615 1.24 0.00 36.14 2.83
2531 15214 8.623030 CAAACCACATGGAAATCATTTTTCTTT 58.377 29.630 4.53 0.00 38.94 2.52
2588 15271 6.428159 ACTCTTGTCTTTTGCCAACTGTATAG 59.572 38.462 0.00 0.00 0.00 1.31
2609 15292 0.320073 TTCAGCTTTGGGGACGTACG 60.320 55.000 15.01 15.01 0.00 3.67
2640 15323 1.003718 GTGCGGTAGAAAGGTGGCT 60.004 57.895 0.00 0.00 0.00 4.75
2672 15355 3.454573 CGCATGCTGGTTGGCCAT 61.455 61.111 17.13 0.00 45.05 4.40
2681 15364 2.879756 GCTGGTTGGCCATAGTGAGAAA 60.880 50.000 6.09 0.00 45.05 2.52
2682 15365 3.012518 CTGGTTGGCCATAGTGAGAAAG 58.987 50.000 6.09 0.00 45.05 2.62
2692 15375 6.808704 GGCCATAGTGAGAAAGTTTTTGATTC 59.191 38.462 0.00 0.00 0.00 2.52
2739 15422 8.795786 TGGAAGTGAGACATTTTTATTTTTCG 57.204 30.769 0.00 0.00 0.00 3.46
2868 17053 6.834107 AGATGGATATGATGTTCATGTGACA 58.166 36.000 7.04 7.04 37.70 3.58
2875 17060 4.602107 TGATGTTCATGTGACATGGGAAT 58.398 39.130 23.88 14.71 0.00 3.01
2881 17066 6.014413 TGTTCATGTGACATGGGAATGATTTT 60.014 34.615 23.88 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.415200 CTACCCCAGGCTTAGGACTC 58.585 60.000 6.57 0.00 0.00 3.36
682 2379 5.180492 TCCACCACATGAAATTAAGAACGTC 59.820 40.000 0.00 0.00 0.00 4.34
886 5228 2.159585 CGCTTTGTGTTGTGAACTGACA 60.160 45.455 0.00 0.00 0.00 3.58
1273 5644 3.058160 CCTGCTCCCTTGGCAACG 61.058 66.667 0.00 0.00 39.30 4.10
1510 5884 0.108186 TTGCTATGCCACTCTCACCG 60.108 55.000 0.00 0.00 0.00 4.94
1864 14000 2.751436 CCACCATTGCCAGACCCG 60.751 66.667 0.00 0.00 0.00 5.28
2086 14232 6.642950 GCGATTACATGTTAGTAGATTGCTCT 59.357 38.462 2.30 0.00 35.39 4.09
2218 14373 0.598562 AGGATGACGAATAGCGCGAT 59.401 50.000 12.10 5.99 46.04 4.58
2308 14463 5.044772 TCAGGCTGTAATTTTACCCCACATA 60.045 40.000 15.27 0.00 32.72 2.29
2361 14516 8.076178 AGTAATATTATGACGCTCCATTTTTGC 58.924 33.333 0.00 0.00 0.00 3.68
2469 14624 5.488561 ACATATGGGCTGACATGGTATGATA 59.511 40.000 7.80 0.00 32.39 2.15
2508 14663 7.507829 TCAAAGAAAAATGATTTCCATGTGGT 58.492 30.769 0.00 0.00 35.24 4.16
2531 15214 3.996363 CACGTGGATGTCATCTTTCTTCA 59.004 43.478 7.95 0.00 0.00 3.02
2588 15271 1.534163 GTACGTCCCCAAAGCTGAAAC 59.466 52.381 0.00 0.00 0.00 2.78
2609 15292 3.998341 TCTACCGCACCTTAATGTGTTTC 59.002 43.478 11.79 0.00 38.52 2.78
2774 15463 7.443272 GTCACATGAACATCATATCCATCTCAA 59.557 37.037 0.00 0.00 34.28 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.